PART III INFORMATION PATHWAYS Three major processes in cellular utilization of genetic information o Replication the copying of parental DNA to form daughter DNA molecules with identical nucleotide sequences o Transcription the process by which parts of the genetic message encoded in DNA are copied precisely into RNA o Translation the genetic message encoded in messenger RNA is translated on the ribosomes into a polypeptide with a particular sequence of amino acids The ribosome most of the translational apparatus and some parts of the transcriptional machinery are shared by every living organism on this planet Chapter 24 Genes and Chromosomes Chromosomes the repositories of genetic information 24 1 Chromosomal Elements Genes Are Segments of DNA That Code for Polypeptide Chains and RNAs a hypothesis in which it was believed that each gene visible property damage and alterations in the DNA sequence Phenotype Mutations One gene one enzyme coded for one enzyme One gene one polypeptide enzyme or for one polypeptide of a multisubunit protein Gene product denote the beginning or end of genes or influence the transcription of genes or function as initiation points for replication or recombination all the DNA that encodes the primary sequence of some final gene segments of DNA that provide signals that may many genes code for a protein that is not an Regulatory sequences DNA Molecules Are Much Longer Than the Cellular or Viral Packages That Contain Them Viruses o Not free living organisms o Infectious parasites that use the resources of a host cell to carry out many of the processes they require to propagate o Have RNA genomes that are particularly small o Genomes of DNA viruses vary greatly in size Many are circular for at least part of their life cycle specific types of viral DNA o Replicative forms Bacteria o Circular DNA chromosome in the nucleoid o Many bacteria contain one or more small circular DNA molecules that are free in the cytosol called plasmids Carry genetic information Undergo replication to yield daughter plasmids Eukaryotes o Humans have 46 chromosomes o Mitochondria and chloroplasts also contain DNA MtDNA is much smaller than nuclear DNA MtDNA is circular Eukaryotic Genes and Chromosomes Are Very Complex The nucleotide sequences of many eukaryotic genes contain one or more intervening segments of DNA that do not code for the amino acid sequence of the polypeptide product o Intervening sequences o Exons o In higher eukaryotes there are more introns than exons coding segments or introns Highly repetitive repeats SSR sequences that are repeated millions of times per cell sequences simple sequence DNA or simple sequence o Generally less than 10 bp o Also called satellite DNA o Do not encode proteins or RNAs a sequence of DNA that functions during cell division as an Centromere attachment point for proteins that link the chromosome to the mitotic spindle o Essential for the distribution of DNA to the daughter cells o Rich in A T pairs sequences at the ends of eukaryotic chromosomes that help Telomeres stabilize the chromosome o Added by telomerase 24 2 DNA Supercoiling Supercoiling the coiling of a coil o Generally a manifestation of structural strain when there is no net bending of the DNA axis Relaxed Replication and transcription of DNA are affected by supercoiling Supercoiling is an intrinsic property of DNA tertiary structure Topology continuous deformations the study of the properties of an object that do not change under o Continuous deformations include conformational changes due to thermal motion or an interaction with proteins or other molecules o Discontinuous deformations involve DNA strand breakage Most Cellular DNA Is Underwound Closed circular DNAs either strand o Rarely relaxed plasmids and small viral DNAs that have no breaks in Underwinding causes strain by having fewer helical turns than expected DNA Underwinding Is Defined by Topological Linking Number Linking number a topological property of double stranded DNA o Does not vary when the DNA is bent or deformed as long as both strands remain intact o Undefined if there are breaks in the DNA or superhelical density a measure of the Specific linking difference number of turns removed relative to the number present in relaxed DNA o Generally in the range of 0 05 to 0 07 o Negative sign means change is due to underwinding two forms of a circular DNA that differ only in a topological Topoisomers property such as linking number Two components of linking number Tw determining the local twisting or spatial relationship of o Twist neighboring base pairs o Writhe o Geometric properties Wr a measure of the coiling of the helix axis Underwinding causes supercoiling makes strand separation easier and facilitates structural changes in the molecule Topoisomerases Catalyze Changes in the Linking Number of DNA enzymes that increase or decrease the extent of DNA Topoisomerases underwinding o Change the linking number o Important in replication and DNA packaging o Two classes Type I topoisomerases strands passing the unbroken strand through the break and rejoining the broken ends transiently break one of the two DNA Change Lk in increments of 1 Type II topoisomerases Lk in increments of 2 break both DNA strands and change DNA Compaction Requires a Special Form of Supercoiling Supercoils are right handed in a negatively supercoiled DNA molecule Plectonemic regular way any structure with strands intertwined in some simple and o Does not produce significant packaging o More stable in solution Solenoidal DNA a form of supercoiling that can be adopted by an underwound o Involves tight left handed turns o Can be stabilized by protein binding o Found in chromatin provides a much greater degree of packing 24 3 The Structure of Chromosomes Chromatin Consists of DNA and Proteins Chromatin the chromosomal material o Consists of fibers containing protein and DNA with small amounts of proteins that package and order the DNA into structural units RNA Histones called nucleosomes Histones Are Small Basic Proteins Histones are rich in basic amino acids arginine and lysine Five major classes in eukaryotic cells o H3 identical in all eukaryotes o H4 identical in all eukaryotes o H1 o H2A o H2B Histones are subject to enzymatic modification by o Methylation o Acetylation o ADP ribosylation o Phosphorylation o Glycosylation o Sumoylation o Ubiquitonation order packing of chromatin is built o Contain eight histones Two H2A Two H2B Two H3 Two H4
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